NMDS for Reference streams
19 July, 2021
R version 4.0.3 (2020-10-10) – “Bunny-Wunnies Freak Out”
Packages used for NMDS: vegan (version 2.5-7)
Methods
The document shows a series of NMDS ordinations for reference benthic communities in Virginia with environmental characteristics overlaid to evaluate natural differences in community compositions across Virginia. These NMDS will support the Genus level IBI development process. This analysis is the first run of all of reference sites in Virginia. No West Virginia DEP data is used in this analysis.Reference sites were evaluated by regional biologists.
The dataset used includes all reference stations collected in Virginia that were deemed reference through a series or water quality parameter filters and regional biologist review. If stations appeared in the dataset more than 4 times, then the most recent 4 samples were used and the rest removed. Samples that had a total number of taxa below 100 collected at the time of sampling were also removed. Taxa that occurred in the dataset <= 5% of the time were removed. The data was log10 +1 transformed. Environmental factors were compiled for each station and used to plot over the NMDS to show environmental variation associated with the community matrix. The envfit function in Vegan was used to plot the continuous environmental variables. Some environmental variables like precipitation, slope, and elevation have not been calculated for all watersheds yet and will be added at a later date.
The first step was to read in the reference site bug taxa list and environmental factors dataset for each station. Join the environmental dataset with the bug dataset to account for multiple observations of each station and collection date and time.
Check to make sure the bug and environmental join was successful:
Number of rows in Community Matrix: 854
Number or rows in Environmental Matrix: 858
The data was log10+1 transformed. Rare taxa (<=5%) were removed.
Run NMDS for reference communities
## Run 0 stress 0.1680316
## Run 1 stress 0.1682788
## ... Procrustes: rmse 0.002094253 max resid 0.03929038
## Run 2 stress 0.1680344
## ... Procrustes: rmse 0.0004153133 max resid 0.01078579
## Run 3 stress 0.1683903
## ... Procrustes: rmse 0.003248783 max resid 0.06894173
## Run 4 stress 0.168319
## ... Procrustes: rmse 0.002503255 max resid 0.06040464
## Run 5 stress 0.1683556
## ... Procrustes: rmse 0.003476846 max resid 0.06725868
## Run 6 stress 0.1683339
## ... Procrustes: rmse 0.002847058 max resid 0.06607347
## Run 7 stress 0.1680899
## ... Procrustes: rmse 0.001417277 max resid 0.03955295
## Run 8 stress 0.1682728
## ... Procrustes: rmse 0.002491595 max resid 0.06609344
## Run 9 stress 0.1686452
## Run 10 stress 0.1680892
## ... Procrustes: rmse 0.002714453 max resid 0.06717377
## Run 11 stress 0.1681425
## ... Procrustes: rmse 0.00326077 max resid 0.06699139
## Run 12 stress 0.1682982
## ... Procrustes: rmse 0.002702858 max resid 0.06610534
## Run 13 stress 0.1686129
## Run 14 stress 0.1680725
## ... Procrustes: rmse 0.002477047 max resid 0.0671894
## Run 15 stress 0.1681831
## ... Procrustes: rmse 0.002876592 max resid 0.06717081
## Run 16 stress 0.1681687
## ... Procrustes: rmse 0.002906909 max resid 0.06718772
## Run 17 stress 0.1683696
## ... Procrustes: rmse 0.003309548 max resid 0.07293241
## Run 18 stress 0.1691898
## Run 19 stress 0.1681206
## ... Procrustes: rmse 0.002863114 max resid 0.067171
## Run 20 stress 0.1681092
## ... Procrustes: rmse 0.001021701 max resid 0.02919367
## Run 21 stress 0.168298
## ... Procrustes: rmse 0.002682323 max resid 0.06610088
## Run 22 stress 0.1683778
## ... Procrustes: rmse 0.003910262 max resid 0.06903507
## Run 23 stress 0.1683244
## ... Procrustes: rmse 0.003343452 max resid 0.06729314
## Run 24 stress 0.1684807
## ... Procrustes: rmse 0.003865168 max resid 0.06715538
## Run 25 stress 0.169514
## Run 26 stress 0.1684814
## ... Procrustes: rmse 0.003848618 max resid 0.06715231
## Run 27 stress 0.169289
## Run 28 stress 0.1681658
## ... Procrustes: rmse 0.003426926 max resid 0.06698674
## Run 29 stress 0.1680551
## ... Procrustes: rmse 0.001040724 max resid 0.02856886
## Run 30 stress 0.1680538
## ... Procrustes: rmse 0.001038796 max resid 0.02857549
## Run 31 stress 0.1681441
## ... Procrustes: rmse 0.003321352 max resid 0.06741241
## Run 32 stress 0.1693094
## Run 33 stress 0.16824
## ... Procrustes: rmse 0.003262915 max resid 0.06704363
## Run 34 stress 0.1684228
## ... Procrustes: rmse 0.00357446 max resid 0.07179115
## Run 35 stress 0.1682921
## ... Procrustes: rmse 0.003543651 max resid 0.06695058
## Run 36 stress 0.1684775
## ... Procrustes: rmse 0.003809401 max resid 0.06713317
## Run 37 stress 0.168377
## ... Procrustes: rmse 0.002876497 max resid 0.06607131
## Run 38 stress 0.1681627
## ... Procrustes: rmse 0.002655034 max resid 0.06986516
## Run 39 stress 0.1686123
## Run 40 stress 0.1682991
## ... Procrustes: rmse 0.002711606 max resid 0.06610247
## Run 41 stress 0.1684786
## ... Procrustes: rmse 0.004146116 max resid 0.06795961
## Run 42 stress 0.168388
## ... Procrustes: rmse 0.003447387 max resid 0.06796976
## Run 43 stress 0.1683201
## ... Procrustes: rmse 0.00244713 max resid 0.05802175
## Run 44 stress 0.1682266
## ... Procrustes: rmse 0.002934022 max resid 0.07028475
## Run 45 stress 0.1684676
## ... Procrustes: rmse 0.004278469 max resid 0.06942797
## Run 46 stress 0.1691862
## Run 47 stress 0.1691956
## Run 48 stress 0.1680283
## ... New best solution
## ... Procrustes: rmse 0.002329312 max resid 0.06725454
## Run 49 stress 0.1691409
## Run 50 stress 0.1686419
## Run 51 stress 0.1682766
## ... Procrustes: rmse 0.003407427 max resid 0.06717619
## Run 52 stress 0.1681203
## ... Procrustes: rmse 0.001665005 max resid 0.03912249
## Run 53 stress 0.1683864
## ... Procrustes: rmse 0.004184016 max resid 0.07025636
## Run 54 stress 0.1682409
## ... Procrustes: rmse 0.002290375 max resid 0.06602828
## Run 55 stress 0.1685029
## ... Procrustes: rmse 0.003175804 max resid 0.06615834
## Run 56 stress 0.1683103
## ... Procrustes: rmse 0.003955485 max resid 0.07293926
## Run 57 stress 0.168292
## ... Procrustes: rmse 0.002668537 max resid 0.06602745
## Run 58 stress 0.1686322
## Run 59 stress 0.1685292
## Run 60 stress 0.1683903
## ... Procrustes: rmse 0.004084701 max resid 0.07271625
## Run 61 stress 0.1683325
## ... Procrustes: rmse 0.003658022 max resid 0.06729705
## Run 62 stress 0.168195
## ... Procrustes: rmse 0.003737942 max resid 0.07310167
## Run 63 stress 0.1686157
## Run 64 stress 0.1681361
## ... Procrustes: rmse 0.002750963 max resid 0.06698494
## Run 65 stress 0.168202
## ... Procrustes: rmse 0.002789287 max resid 0.06811055
## Run 66 stress 0.1692724
## Run 67 stress 0.168593
## Run 68 stress 0.1680871
## ... Procrustes: rmse 0.001382354 max resid 0.03941065
## Run 69 stress 0.1681191
## ... Procrustes: rmse 0.001655762 max resid 0.03911604
## Run 70 stress 0.1683553
## ... Procrustes: rmse 0.002565417 max resid 0.05666184
## Run 71 stress 0.1680512
## ... Procrustes: rmse 0.001031455 max resid 0.02858086
## Run 72 stress 0.1685326
## Run 73 stress 0.1684131
## ... Procrustes: rmse 0.004358423 max resid 0.07218529
## Run 74 stress 0.1681085
## ... Procrustes: rmse 0.001057714 max resid 0.02896322
## Run 75 stress 0.1686138
## Run 76 stress 0.1692837
## Run 77 stress 0.1684436
## ... Procrustes: rmse 0.00437138 max resid 0.06962612
## Run 78 stress 0.1682932
## ... Procrustes: rmse 0.002687593 max resid 0.06603679
## Run 79 stress 0.1680878
## ... Procrustes: rmse 0.001389963 max resid 0.03942231
## Run 80 stress 0.1682403
## ... Procrustes: rmse 0.002279635 max resid 0.0660476
## Run 81 stress 0.1683323
## ... Procrustes: rmse 0.002818026 max resid 0.06600887
## Run 82 stress 0.1685314
## Run 83 stress 0.1680289
## ... Procrustes: rmse 0.0001531666 max resid 0.003420264
## ... Similar to previous best
## *** Solution reached##
## Call:
## metaMDS(comm = NMDSFive[, 6:119], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NMDSFive[, 6:119]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1680283
## Stress type 1, weak ties
## Two convergent solutions found after 83 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NMDSFive[, 6:119]'
Envfit results from Vegan package :
##
## ***VECTORS
##
## NMDS1 NMDS2 r2 Pr(>r)
## JulianDate -0.74577 -0.66620 0.0796 0.650
## Latitude 0.92022 0.39141 0.2422 0.233
## Longitude 0.88288 -0.46960 0.2478 0.188
## US_L3CODE 0.33173 0.94337 0.3232 0.118
## Order -0.84966 0.52734 0.7362 0.002 **
## EDASOrder -0.84966 0.52734 0.7362 0.002 **
## totalArea_sqMile -0.22776 0.97372 0.4460 0.056 .
## ELEVMEAN -0.62319 0.78207 0.5263 0.016 *
## SLPMEAN -0.17953 0.98375 0.7846 0.001 ***
## wshdRain_mmyr -0.20341 0.97909 0.4501 0.052 .
## siteRain_mmyr -0.63132 -0.77552 0.2593 0.208
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
##
## ***FACTORS:
##
## Centroids:
## NMDS1 NMDS2
## SeasonFall -0.6888 -0.5964
## SeasonOutside Sample Window -0.5886 -0.1171
## SeasonSpring -0.6517 -0.2768
## GradientMACS -0.6631 -0.4023
## CoastalTRUE -0.6631 -0.4023
## US_L3NAMEMiddle Atlantic Coastal Plain -0.6508 -0.6875
## US_L3NAMESoutheastern Plains -0.6699 -0.2439
## US_L4NAMEChesapeake-Pamlico Lowlands and Tidal Marshes -0.6785 -0.3700
## US_L4NAMEMid-Atlantic Flatwoods -0.6324 -0.8991
## US_L4NAMERolling Coastal Plain -0.6699 -0.2439
## ASSESS_REGPRO -0.6715 -0.2669
## ASSESS_REGTRO -0.6324 -0.8991
## TidalN -0.6605 -0.4077
## TidalT -0.6785 -0.3700
## VAHUSBCB -0.6025 -0.5413
## VAHUSBCU -0.7189 -0.5304
## VAHUSBYO -0.6400 -0.0712
## BasinChes. Bay and Small Coastal Basin -0.6025 -0.5413
## BasinChowan and Dismal Swamp River Basin -0.7189 -0.5304
## BasinYork River Basin -0.6400 -0.0712
## Basin_CodeChowan-Dismal -0.7189 -0.5304
## Basin_CodeSmall Coastal -0.6025 -0.5413
## Basin_CodeYork -0.6400 -0.0712
## CountyCityNameCaroline -0.6972 -0.0029
## CountyCityNameDinwiddie -0.8401 -0.3514
## CountyCityNameHanover -0.5828 -0.1395
## CountyCityNameKing and Queen -0.5265 -0.7126
## CountyCityNameNorthumberland -0.6785 -0.3700
## CountyCityNameSouthampton -0.6324 -0.8991
## CountyCityNameSussex -0.7359 0.2176
## WQS_CLASSIII -0.6975 -0.1056
## WQS_CLASSVII -0.6440 -0.5672
## WQS_SPSTDS -0.6484 -0.3599
## WQS_SPSTDSNEW-21 -0.8542 -0.9541
## WQS_PWS -0.6631 -0.4023
## WQS_TROUT -0.6631 -0.4023
## WQS_TIER_III -0.6631 -0.4023
##
## Goodness of fit:
## r2 Pr(>r)
## Season 0.1940 0.350
## Gradient 0.0000 1.000
## Coastal 0.0000 1.000
## US_L3NAME 0.2871 0.049 *
## US_L4NAME 0.4406 0.023 *
## ASSESS_REG 0.4287 0.002 **
## Tidal 0.0014 1.000
## VAHUSB 0.2945 0.136
## Basin 0.2945 0.136
## Basin_Code 0.2945 0.136
## CountyCityName 0.8637 0.002 **
## WQS_CLASS 0.3145 0.031 *
## WQS_SPSTDS 0.1664 0.277
## WQS_PWS 0.0000 1.000
## WQS_TROUT 0.0000 1.000
## WQS_TIER_III 0.0000 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 999
##
## 840 observations deleted due to missingnessPlot with Station IDs
Plot with Axis 3
Plot with Species
Season
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Outside Sample Window Spring
## delta 0.6657 0.6767 0.6705
## n 414 13 427
##
## Chance corrected within-group agreement A: 0.03488
## Based on observed delta 0.6682 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Season with continuous variable vectors
Ecoregion
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Middle Atlantic Coastal Plain
## delta 0.5959 0.6067 0.5814
## n 154 40 25
## Northern Piedmont Piedmont Ridge and Valley Southeastern Plains
## delta 0.6438 0.6146 0.6565 0.6313
## n 101 138 259 137
##
## Chance corrected within-group agreement A: 0.09192
## Based on observed delta 0.6287 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Basin
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Lower James-Middle James-Upper New
## delta 0.5705 0.6551 0.6154 0.6112 0.651 0.6513
## n 15 33 36 61 120 78
## Potomac-Lower Potomac-Shenandoah Rappahannock Roanoke Small Coastal
## delta 0.6837 0.6577 0.667 0.6104 0.5674
## n 31 42 144 87 21
## Tennessee-Big Sandy Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.6048 0.6297 0.6265 0.5709 0.6611
## n 16 50 53 4 63
##
## Chance corrected within-group agreement A: 0.07538
## Based on observed delta 0.6402 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Admin Region
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO TRO VRO
## delta 0.6422 0.69 0.6331 0.6348 0.5719 0.6433
## n 250 195 122 156 21 110
##
## Chance corrected within-group agreement A: 0.06284
## Based on observed delta 0.6489 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Sample Method
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.6384 0.6557
## n 163 691
##
## Chance corrected within-group agreement A: 0.0578
## Based on observed delta 0.6524 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999BioRegion
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$Bioregion, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Coast Mountain Piedmont
## delta 0.6401 0.6479 0.6371
## n 162 453 239
##
## Chance corrected within-group agreement A: 0.07074
## Based on observed delta 0.6434 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
Stream Order
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5 6
## delta 0.6688 0.684 0.658 0.6559 0.6187 0.4221
## n 277 248 172 114 41 2
##
## Chance corrected within-group agreement A: 0.03762
## Based on observed delta 0.6663 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Water Quality Standard Class
##
## Call:
## mrpp(dat = bugsnms[, 6:119], grouping = samplescoresenv$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI VII
## delta 0.6885 0.6448 0.6325 0.6044 0.6293
## n 331 185 87 209 42
##
## Chance corrected within-group agreement A: 0.06143
## Based on observed delta 0.6498 and expected delta 0.6924
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Natural Trout Water WQS?
Based on the observations from the Ecoregion plots, we removed the coastal streams to better assess patterns in the non-coastal streams. The plots below represent streams within all ecoregions except Mid-Atlantic Coastal Plains and Southeastern Plains ecoregions.
NMDS Results for Non-Coastal Streams
## Run 0 stress 0.17744
## Run 1 stress 0.1784171
## Run 2 stress 0.1783329
## Run 3 stress 0.1777508
## ... Procrustes: rmse 0.004307847 max resid 0.09003825
## Run 4 stress 0.1774347
## ... New best solution
## ... Procrustes: rmse 0.002982365 max resid 0.06812756
## Run 5 stress 0.1778972
## ... Procrustes: rmse 0.003762444 max resid 0.06823189
## Run 6 stress 0.1780263
## Run 7 stress 0.1777946
## ... Procrustes: rmse 0.004003507 max resid 0.05565195
## Run 8 stress 0.1786189
## Run 9 stress 0.1786334
## Run 10 stress 0.1780396
## Run 11 stress 0.1782811
## Run 12 stress 0.1784525
## Run 13 stress 0.1778976
## ... Procrustes: rmse 0.002569069 max resid 0.06103171
## Run 14 stress 0.1782683
## Run 15 stress 0.1778561
## ... Procrustes: rmse 0.004250338 max resid 0.06908033
## Run 16 stress 0.1779556
## Run 17 stress 0.1782993
## Run 18 stress 0.1780685
## Run 19 stress 0.1778012
## ... Procrustes: rmse 0.004690843 max resid 0.09185521
## Run 20 stress 0.1779297
## ... Procrustes: rmse 0.00521247 max resid 0.0886128
## Run 21 stress 0.1781129
## Run 22 stress 0.1794492
## Run 23 stress 0.1780772
## Run 24 stress 0.1789266
## Run 25 stress 0.1784087
## Run 26 stress 0.1781172
## Run 27 stress 0.1780046
## Run 28 stress 0.1781762
## Run 29 stress 0.1778117
## ... Procrustes: rmse 0.004728721 max resid 0.08929739
## Run 30 stress 0.1776147
## ... Procrustes: rmse 0.003486044 max resid 0.05542798
## Run 31 stress 0.1784172
## Run 32 stress 0.1782849
## Run 33 stress 0.1781162
## Run 34 stress 0.1774142
## ... New best solution
## ... Procrustes: rmse 0.0022623 max resid 0.04730532
## Run 35 stress 0.1795702
## Run 36 stress 0.1787518
## Run 37 stress 0.1778866
## ... Procrustes: rmse 0.004330808 max resid 0.06902238
## Run 38 stress 0.1777182
## ... Procrustes: rmse 0.003575533 max resid 0.05543604
## Run 39 stress 0.1795867
## Run 40 stress 0.1785558
## Run 41 stress 0.1779837
## Run 42 stress 0.1779223
## Run 43 stress 0.177891
## ... Procrustes: rmse 0.003334076 max resid 0.06094143
## Run 44 stress 0.1774459
## ... Procrustes: rmse 0.002759176 max resid 0.06779705
## Run 45 stress 0.1779408
## Run 46 stress 0.1783388
## Run 47 stress 0.177889
## ... Procrustes: rmse 0.004396002 max resid 0.06903678
## Run 48 stress 0.1777829
## ... Procrustes: rmse 0.004239582 max resid 0.08961911
## Run 49 stress 0.1779356
## Run 50 stress 0.1782501
## Run 51 stress 0.1782891
## Run 52 stress 0.1790799
## Run 53 stress 0.1790663
## Run 54 stress 0.1779609
## Run 55 stress 0.1784598
## Run 56 stress 0.1776627
## ... Procrustes: rmse 0.003316321 max resid 0.06837761
## Run 57 stress 0.1788312
## Run 58 stress 0.178437
## Run 59 stress 0.1782716
## Run 60 stress 0.1778808
## ... Procrustes: rmse 0.003647704 max resid 0.05711445
## Run 61 stress 0.1780623
## Run 62 stress 0.1783403
## Run 63 stress 0.1784587
## Run 64 stress 0.1779288
## Run 65 stress 0.1821683
## Run 66 stress 0.177897
## ... Procrustes: rmse 0.004142218 max resid 0.06837555
## Run 67 stress 0.1782731
## Run 68 stress 0.1779054
## ... Procrustes: rmse 0.003731147 max resid 0.06772671
## Run 69 stress 0.1781444
## Run 70 stress 0.1779256
## Run 71 stress 0.1787302
## Run 72 stress 0.1784463
## Run 73 stress 0.1779305
## Run 74 stress 0.1784613
## Run 75 stress 0.1782945
## Run 76 stress 0.1775938
## ... Procrustes: rmse 0.003423145 max resid 0.06751196
## Run 77 stress 0.1779713
## Run 78 stress 0.1785273
## Run 79 stress 0.1783329
## Run 80 stress 0.1784615
## Run 81 stress 0.1783269
## Run 82 stress 0.178277
## Run 83 stress 0.1780913
## Run 84 stress 0.1780447
## Run 85 stress 0.177914
## ... Procrustes: rmse 0.003806828 max resid 0.06759344
## Run 86 stress 0.1774365
## ... Procrustes: rmse 0.002263225 max resid 0.04758738
## Run 87 stress 0.185868
## Run 88 stress 0.1780101
## Run 89 stress 0.1793987
## Run 90 stress 0.1799688
## Run 91 stress 0.1786506
## Run 92 stress 0.1783016
## Run 93 stress 0.1791376
## Run 94 stress 0.1784763
## Run 95 stress 0.1780269
## Run 96 stress 0.1782843
## Run 97 stress 0.1783742
## Run 98 stress 0.1781034
## Run 99 stress 0.1839784
## Run 100 stress 0.1778139
## ... Procrustes: rmse 0.002912429 max resid 0.05535546
## Run 101 stress 0.1781834
## Run 102 stress 0.1790572
## Run 103 stress 0.178654
## Run 104 stress 0.1781912
## Run 105 stress 0.1785159
## Run 106 stress 0.1782913
## Run 107 stress 0.1778841
## ... Procrustes: rmse 0.003316612 max resid 0.04938054
## Run 108 stress 0.178188
## Run 109 stress 0.1778682
## ... Procrustes: rmse 0.002457582 max resid 0.06072465
## Run 110 stress 0.1777863
## ... Procrustes: rmse 0.002804242 max resid 0.05651219
## Run 111 stress 0.17788
## ... Procrustes: rmse 0.002532096 max resid 0.06064833
## Run 112 stress 0.1779002
## ... Procrustes: rmse 0.004164486 max resid 0.08904178
## Run 113 stress 0.1776335
## ... Procrustes: rmse 0.003882855 max resid 0.06884333
## Run 114 stress 0.1857658
## Run 115 stress 0.1776083
## ... Procrustes: rmse 0.00264426 max resid 0.04839421
## Run 116 stress 0.1780867
## Run 117 stress 0.1782857
## Run 118 stress 0.1785998
## Run 119 stress 0.1778781
## ... Procrustes: rmse 0.003157771 max resid 0.06096905
## Run 120 stress 0.1782872
## Run 121 stress 0.1781925
## Run 122 stress 0.1779878
## Run 123 stress 0.1783347
## Run 124 stress 0.1790077
## Run 125 stress 0.1776339
## ... Procrustes: rmse 0.002847527 max resid 0.0479474
## Run 126 stress 0.1777983
## ... Procrustes: rmse 0.004230606 max resid 0.08567735
## Run 127 stress 0.1784411
## Run 128 stress 0.1782196
## Run 129 stress 0.1780924
## Run 130 stress 0.1782788
## Run 131 stress 0.1780823
## Run 132 stress 0.1778525
## ... Procrustes: rmse 0.00478574 max resid 0.05547993
## Run 133 stress 0.1788025
## Run 134 stress 0.1776255
## ... Procrustes: rmse 0.003338318 max resid 0.06829975
## Run 135 stress 0.1780231
## Run 136 stress 0.1790696
## Run 137 stress 0.178139
## Run 138 stress 0.1793426
## Run 139 stress 0.1779634
## Run 140 stress 0.178172
## Run 141 stress 0.1778969
## ... Procrustes: rmse 0.004132336 max resid 0.06804922
## Run 142 stress 0.1798712
## Run 143 stress 0.1778845
## ... Procrustes: rmse 0.00321301 max resid 0.06075178
## Run 144 stress 0.1785255
## Run 145 stress 0.1774338
## ... Procrustes: rmse 0.002742281 max resid 0.06816
## Run 146 stress 0.1787444
## Run 147 stress 0.1780339
## Run 148 stress 0.1782894
## Run 149 stress 0.1774342
## ... Procrustes: rmse 0.002643227 max resid 0.06800731
## Run 150 stress 0.1783023
## Run 151 stress 0.1778689
## ... Procrustes: rmse 0.002437928 max resid 0.06068653
## Run 152 stress 0.1781743
## Run 153 stress 0.1784816
## Run 154 stress 0.1779589
## Run 155 stress 0.1781368
## Run 156 stress 0.1777029
## ... Procrustes: rmse 0.003553552 max resid 0.09061413
## Run 157 stress 0.1780595
## Run 158 stress 0.1778818
## ... Procrustes: rmse 0.00471838 max resid 0.0911247
## Run 159 stress 0.1793438
## Run 160 stress 0.1775681
## ... Procrustes: rmse 0.00279078 max resid 0.05556893
## Run 161 stress 0.178465
## Run 162 stress 0.1780125
## Run 163 stress 0.1778717
## ... Procrustes: rmse 0.004567118 max resid 0.08763971
## Run 164 stress 0.177592
## ... Procrustes: rmse 0.003129519 max resid 0.05540819
## Run 165 stress 0.1778762
## ... Procrustes: rmse 0.003190632 max resid 0.06070123
## Run 166 stress 0.178027
## Run 167 stress 0.1780347
## Run 168 stress 0.1781443
## Run 169 stress 0.1785971
## Run 170 stress 0.177847
## ... Procrustes: rmse 0.00285822 max resid 0.04866631
## Run 171 stress 0.177576
## ... Procrustes: rmse 0.002874942 max resid 0.05530632
## Run 172 stress 0.1779793
## Run 173 stress 0.1778247
## ... Procrustes: rmse 0.003868073 max resid 0.05541048
## Run 174 stress 0.1795238
## Run 175 stress 0.1779827
## Run 176 stress 0.1793395
## Run 177 stress 0.177924
## Run 178 stress 0.1779813
## Run 179 stress 0.1780706
## Run 180 stress 0.1775885
## ... Procrustes: rmse 0.002869253 max resid 0.03851982
## Run 181 stress 0.1783897
## Run 182 stress 0.1779305
## Run 183 stress 0.178282
## Run 184 stress 0.1782311
## Run 185 stress 0.1783579
## Run 186 stress 0.1792913
## Run 187 stress 0.1779124
## ... Procrustes: rmse 0.004768294 max resid 0.06946542
## Run 188 stress 0.1782739
## Run 189 stress 0.178217
## Run 190 stress 0.1781766
## Run 191 stress 0.1777976
## ... Procrustes: rmse 0.003792133 max resid 0.05564062
## Run 192 stress 0.1782567
## Run 193 stress 0.1787405
## Run 194 stress 0.1780276
## Run 195 stress 0.1780499
## Run 196 stress 0.1775901
## ... Procrustes: rmse 0.003139729 max resid 0.05540281
## Run 197 stress 0.1784211
## Run 198 stress 0.1784794
## Run 199 stress 0.1775816
## ... Procrustes: rmse 0.003145426 max resid 0.05544862
## Run 200 stress 0.1784613
## Run 201 stress 0.1796578
## Run 202 stress 0.1785798
## Run 203 stress 0.178635
## Run 204 stress 0.1782726
## Run 205 stress 0.1784293
## Run 206 stress 0.1781836
## Run 207 stress 0.1783071
## Run 208 stress 0.178279
## Run 209 stress 0.1777628
## ... Procrustes: rmse 0.003061503 max resid 0.05542911
## Run 210 stress 0.1782136
## Run 211 stress 0.1787183
## Run 212 stress 0.1782095
## Run 213 stress 0.1793385
## Run 214 stress 0.1784389
## Run 215 stress 0.1778258
## ... Procrustes: rmse 0.003928312 max resid 0.05550561
## Run 216 stress 0.1789712
## Run 217 stress 0.1810845
## Run 218 stress 0.1780378
## Run 219 stress 0.1782988
## Run 220 stress 0.1783106
## Run 221 stress 0.1778762
## ... Procrustes: rmse 0.003113338 max resid 0.06067142
## Run 222 stress 0.1783859
## Run 223 stress 0.1806004
## Run 224 stress 0.1779567
## Run 225 stress 0.1785157
## Run 226 stress 0.1795303
## Run 227 stress 0.177773
## ... Procrustes: rmse 0.003751573 max resid 0.08949127
## Run 228 stress 0.1778577
## ... Procrustes: rmse 0.004420555 max resid 0.06916661
## Run 229 stress 0.1784449
## Run 230 stress 0.1780994
## Run 231 stress 0.1786013
## Run 232 stress 0.1786654
## Run 233 stress 0.1781751
## Run 234 stress 0.1789564
## Run 235 stress 0.1776197
## ... Procrustes: rmse 0.00406603 max resid 0.0674309
## Run 236 stress 0.1781916
## Run 237 stress 0.1789804
## Run 238 stress 0.1781072
## Run 239 stress 0.182984
## Run 240 stress 0.178062
## Run 241 stress 0.1777738
## ... Procrustes: rmse 0.004214652 max resid 0.05593743
## Run 242 stress 0.1783953
## Run 243 stress 0.1787149
## Run 244 stress 0.1785743
## Run 245 stress 0.1784692
## Run 246 stress 0.177433
## ... Procrustes: rmse 0.002253172 max resid 0.04724468
## Run 247 stress 0.1774289
## ... Procrustes: rmse 0.001920034 max resid 0.04800597
## Run 248 stress 0.1784246
## Run 249 stress 0.1779758
## Run 250 stress 0.1777382
## ... Procrustes: rmse 0.004662629 max resid 0.08496343
## Run 251 stress 0.1787279
## Run 252 stress 0.1778827
## ... Procrustes: rmse 0.004752103 max resid 0.09130003
## Run 253 stress 0.178501
## Run 254 stress 0.1793099
## Run 255 stress 0.1790331
## Run 256 stress 0.1782471
## Run 257 stress 0.1782436
## Run 258 stress 0.1779887
## Run 259 stress 0.1776132
## ... Procrustes: rmse 0.00215936 max resid 0.04832572
## Run 260 stress 0.1779682
## Run 261 stress 0.1779954
## Run 262 stress 0.1779897
## Run 263 stress 0.1781425
## Run 264 stress 0.1774297
## ... Procrustes: rmse 0.001929419 max resid 0.04824752
## Run 265 stress 0.1784791
## Run 266 stress 0.1784616
## Run 267 stress 0.1782833
## Run 268 stress 0.177615
## ... Procrustes: rmse 0.004030955 max resid 0.06758905
## Run 269 stress 0.1784122
## Run 270 stress 0.1779083
## ... Procrustes: rmse 0.005295112 max resid 0.09328088
## Run 271 stress 0.1781383
## Run 272 stress 0.1786335
## Run 273 stress 0.1781181
## Run 274 stress 0.1781765
## Run 275 stress 0.1775578
## ... Procrustes: rmse 0.002606498 max resid 0.05556715
## Run 276 stress 0.1842364
## Run 277 stress 0.1774483
## ... Procrustes: rmse 0.002767599 max resid 0.06779287
## Run 278 stress 0.1780327
## Run 279 stress 0.1775604
## ... Procrustes: rmse 0.002205018 max resid 0.05540155
## Run 280 stress 0.1777128
## ... Procrustes: rmse 0.003901356 max resid 0.08863352
## Run 281 stress 0.1781384
## Run 282 stress 0.178282
## Run 283 stress 0.1796112
## Run 284 stress 0.179715
## Run 285 stress 0.1817327
## Run 286 stress 0.1787442
## Run 287 stress 0.1782143
## Run 288 stress 0.1779624
## Run 289 stress 0.1777298
## ... Procrustes: rmse 0.00464531 max resid 0.06938591
## Run 290 stress 0.1777961
## ... Procrustes: rmse 0.004465824 max resid 0.09007085
## Run 291 stress 0.1788948
## Run 292 stress 0.1779998
## Run 293 stress 0.1777089
## ... Procrustes: rmse 0.003905756 max resid 0.09022439
## Run 294 stress 0.1778944
## ... Procrustes: rmse 0.003528694 max resid 0.06796853
## Run 295 stress 0.1788926
## Run 296 stress 0.1781975
## Run 297 stress 0.1780477
## Run 298 stress 0.1784566
## Run 299 stress 0.1779248
## Run 300 stress 0.1789807
## Run 301 stress 0.1786592
## Run 302 stress 0.1783334
## Run 303 stress 0.1790749
## Run 304 stress 0.1774432
## ... Procrustes: rmse 0.002951549 max resid 0.06806328
## Run 305 stress 0.1776567
## ... Procrustes: rmse 0.002669194 max resid 0.0480324
## Run 306 stress 0.1782582
## Run 307 stress 0.1780717
## Run 308 stress 0.17776
## ... Procrustes: rmse 0.004773926 max resid 0.08528918
## Run 309 stress 0.1786974
## Run 310 stress 0.1783038
## Run 311 stress 0.177986
## Run 312 stress 0.1782861
## Run 313 stress 0.1777148
## ... Procrustes: rmse 0.003976461 max resid 0.09060529
## Run 314 stress 0.1776707
## ... Procrustes: rmse 0.003488494 max resid 0.06678833
## Run 315 stress 0.1781448
## Run 316 stress 0.1777984
## ... Procrustes: rmse 0.00351723 max resid 0.05556409
## Run 317 stress 0.1780075
## Run 318 stress 0.1784855
## Run 319 stress 0.1784946
## Run 320 stress 0.1782654
## Run 321 stress 0.1776079
## ... Procrustes: rmse 0.002694276 max resid 0.0487854
## Run 322 stress 0.178316
## Run 323 stress 0.1782142
## Run 324 stress 0.1779034
## ... Procrustes: rmse 0.003647476 max resid 0.04936929
## Run 325 stress 0.1778844
## ... Procrustes: rmse 0.003357007 max resid 0.06079509
## Run 326 stress 0.1777109
## ... Procrustes: rmse 0.003773226 max resid 0.08954204
## Run 327 stress 0.1779631
## Run 328 stress 0.1782686
## Run 329 stress 0.1788673
## Run 330 stress 0.1775589
## ... Procrustes: rmse 0.00215865 max resid 0.05539507
## Run 331 stress 0.1777967
## ... Procrustes: rmse 0.003004397 max resid 0.05627998
## Run 332 stress 0.1782384
## Run 333 stress 0.1780675
## Run 334 stress 0.1782289
## Run 335 stress 0.1782953
## Run 336 stress 0.1783555
## Run 337 stress 0.1782825
## Run 338 stress 0.179286
## Run 339 stress 0.1781042
## Run 340 stress 0.1781374
## Run 341 stress 0.1779794
## Run 342 stress 0.1780211
## Run 343 stress 0.1782111
## Run 344 stress 0.1780013
## Run 345 stress 0.1777208
## ... Procrustes: rmse 0.003749734 max resid 0.05541595
## Run 346 stress 0.1783645
## Run 347 stress 0.1774197
## ... Procrustes: rmse 0.001691513 max resid 0.03446975
## Run 348 stress 0.1783192
## Run 349 stress 0.1778563
## ... Procrustes: rmse 0.004370002 max resid 0.06909045
## Run 350 stress 0.1781906
## Run 351 stress 0.1779249
## Run 352 stress 0.1782719
## Run 353 stress 0.1809928
## Run 354 stress 0.178388
## Run 355 stress 0.1778979
## ... Procrustes: rmse 0.004169044 max resid 0.06814402
## Run 356 stress 0.1785341
## Run 357 stress 0.178132
## Run 358 stress 0.1785301
## Run 359 stress 0.179162
## Run 360 stress 0.1774227
## ... Procrustes: rmse 0.0009314259 max resid 0.02216944
## Run 361 stress 0.1774275
## ... Procrustes: rmse 0.002000455 max resid 0.04861489
## Run 362 stress 0.1776059
## ... Procrustes: rmse 0.003999221 max resid 0.06775236
## Run 363 stress 0.177923
## Run 364 stress 0.1780623
## Run 365 stress 0.1780882
## Run 366 stress 0.178535
## Run 367 stress 0.1779047
## ... Procrustes: rmse 0.003699803 max resid 0.06773411
## Run 368 stress 0.178074
## Run 369 stress 0.1778058
## ... Procrustes: rmse 0.003697116 max resid 0.06867891
## Run 370 stress 0.1784854
## Run 371 stress 0.1775601
## ... Procrustes: rmse 0.002205214 max resid 0.05540424
## Run 372 stress 0.1776821
## ... Procrustes: rmse 0.004353309 max resid 0.06906327
## Run 373 stress 0.1775816
## ... Procrustes: rmse 0.003106576 max resid 0.0554443
## Run 374 stress 0.1779013
## ... Procrustes: rmse 0.004754162 max resid 0.06930139
## Run 375 stress 0.1776622
## ... Procrustes: rmse 0.00399543 max resid 0.06873316
## Run 376 stress 0.1786111
## Run 377 stress 0.1785076
## Run 378 stress 0.1779927
## Run 379 stress 0.1789589
## Run 380 stress 0.1783671
## Run 381 stress 0.1778945
## ... Procrustes: rmse 0.005276894 max resid 0.06873755
## Run 382 stress 0.1780967
## Run 383 stress 0.1777978
## ... Procrustes: rmse 0.00481022 max resid 0.08250663
## Run 384 stress 0.1779319
## Run 385 stress 0.1777506
## ... Procrustes: rmse 0.003882069 max resid 0.04972472
## Run 386 stress 0.1793708
## Run 387 stress 0.1779847
## Run 388 stress 0.178223
## Run 389 stress 0.1778985
## ... Procrustes: rmse 0.00414251 max resid 0.06804609
## Run 390 stress 0.1778042
## ... Procrustes: rmse 0.004597303 max resid 0.09047564
## Run 391 stress 0.178374
## Run 392 stress 0.1784437
## Run 393 stress 0.1780093
## Run 394 stress 0.1784093
## Run 395 stress 0.1780975
## Run 396 stress 0.1782861
## Run 397 stress 0.1776523
## ... Procrustes: rmse 0.002711146 max resid 0.04920934
## Run 398 stress 0.1784027
## Run 399 stress 0.1779199
## Run 400 stress 0.1778707
## ... Procrustes: rmse 0.002752294 max resid 0.06051968
## Run 401 stress 0.1784073
## Run 402 stress 0.1779554
## Run 403 stress 0.1786429
## Run 404 stress 0.1780975
## Run 405 stress 0.1779957
## Run 406 stress 0.1778296
## ... Procrustes: rmse 0.00501856 max resid 0.09022245
## Run 407 stress 0.1780124
## Run 408 stress 0.184868
## Run 409 stress 0.1784494
## Run 410 stress 0.1778709
## ... Procrustes: rmse 0.00459763 max resid 0.08943464
## Run 411 stress 0.1813091
## Run 412 stress 0.177789
## ... Procrustes: rmse 0.004404661 max resid 0.09167278
## Run 413 stress 0.1780181
## Run 414 stress 0.1776163
## ... Procrustes: rmse 0.004116526 max resid 0.06751025
## Run 415 stress 0.183026
## Run 416 stress 0.1784114
## Run 417 stress 0.1778048
## ... Procrustes: rmse 0.004421672 max resid 0.06832183
## Run 418 stress 0.1778382
## ... Procrustes: rmse 0.003163184 max resid 0.04882685
## Run 419 stress 0.1776405
## ... Procrustes: rmse 0.002916667 max resid 0.0476901
## Run 420 stress 0.1781426
## Run 421 stress 0.1785223
## Run 422 stress 0.1776082
## ... Procrustes: rmse 0.003540753 max resid 0.0674553
## Run 423 stress 0.1775814
## ... Procrustes: rmse 0.003094466 max resid 0.05544215
## Run 424 stress 0.1782987
## Run 425 stress 0.1794185
## Run 426 stress 0.1783387
## Run 427 stress 0.1774934
## ... Procrustes: rmse 0.003663662 max resid 0.06865356
## Run 428 stress 0.1787558
## Run 429 stress 0.1782812
## Run 430 stress 0.1777528
## ... Procrustes: rmse 0.00459604 max resid 0.08954522
## Run 431 stress 0.1779355
## Run 432 stress 0.1786933
## Run 433 stress 0.1781223
## Run 434 stress 0.1782672
## Run 435 stress 0.1781756
## Run 436 stress 0.1918283
## Run 437 stress 0.1776726
## ... Procrustes: rmse 0.003309954 max resid 0.05563828
## Run 438 stress 0.1776754
## ... Procrustes: rmse 0.003533364 max resid 0.05559233
## Run 439 stress 0.178123
## Run 440 stress 0.1782435
## Run 441 stress 0.1779727
## Run 442 stress 0.1783316
## Run 443 stress 0.1774397
## ... Procrustes: rmse 0.003331543 max resid 0.06838491
## Run 444 stress 0.1779872
## Run 445 stress 0.1786414
## Run 446 stress 0.1774421
## ... Procrustes: rmse 0.002276042 max resid 0.04329031
## Run 447 stress 0.1781857
## Run 448 stress 0.1777137
## ... Procrustes: rmse 0.003858535 max resid 0.08627092
## Run 449 stress 0.1782272
## Run 450 stress 0.177786
## ... Procrustes: rmse 0.004621432 max resid 0.07723465
## Run 451 stress 0.1778581
## ... Procrustes: rmse 0.004483803 max resid 0.09292721
## Run 452 stress 0.1775598
## ... Procrustes: rmse 0.002740299 max resid 0.05553449
## Run 453 stress 0.1781406
## Run 454 stress 0.177857
## ... Procrustes: rmse 0.004390727 max resid 0.06913836
## Run 455 stress 0.1775589
## ... Procrustes: rmse 0.002708052 max resid 0.05549934
## Run 456 stress 0.1785736
## Run 457 stress 0.1782782
## Run 458 stress 0.1777589
## ... Procrustes: rmse 0.004712214 max resid 0.08410976
## Run 459 stress 0.1784971
## Run 460 stress 0.1784664
## Run 461 stress 0.1778877
## ... Procrustes: rmse 0.003027147 max resid 0.06099201
## Run 462 stress 0.1780604
## Run 463 stress 0.1784659
## Run 464 stress 0.1777971
## ... Procrustes: rmse 0.003038476 max resid 0.05642175
## Run 465 stress 0.1774288
## ... Procrustes: rmse 0.001507841 max resid 0.03431508
## Run 466 stress 0.1782145
## Run 467 stress 0.1785602
## Run 468 stress 0.1780557
## Run 469 stress 0.1778932
## ... Procrustes: rmse 0.003645917 max resid 0.04979133
## Run 470 stress 0.1778978
## ... Procrustes: rmse 0.004150972 max resid 0.06805727
## Run 471 stress 0.1776112
## ... Procrustes: rmse 0.004079266 max resid 0.06774018
## Run 472 stress 0.1774353
## ... Procrustes: rmse 0.002199734 max resid 0.04443026
## Run 473 stress 0.1776469
## ... Procrustes: rmse 0.003688182 max resid 0.04957709
## Run 474 stress 0.1775768
## ... Procrustes: rmse 0.002913026 max resid 0.05531466
## Run 475 stress 0.177433
## ... Procrustes: rmse 0.00217863 max resid 0.04500018
## Run 476 stress 0.1834674
## Run 477 stress 0.1785257
## Run 478 stress 0.1785025
## Run 479 stress 0.1782794
## Run 480 stress 0.1779242
## Run 481 stress 0.1783641
## Run 482 stress 0.1779779
## Run 483 stress 0.178198
## Run 484 stress 0.17785
## ... Procrustes: rmse 0.004140612 max resid 0.06770213
## Run 485 stress 0.1777163
## ... Procrustes: rmse 0.00365672 max resid 0.06864626
## Run 486 stress 0.1851934
## Run 487 stress 0.1781817
## Run 488 stress 0.1783624
## Run 489 stress 0.1779249
## Run 490 stress 0.1774424
## ... Procrustes: rmse 0.002967407 max resid 0.0681913
## Run 491 stress 0.1779342
## Run 492 stress 0.178013
## Run 493 stress 0.1784422
## Run 494 stress 0.1785996
## Run 495 stress 0.1776447
## ... Procrustes: rmse 0.001866816 max resid 0.04589826
## Run 496 stress 0.178457
## Run 497 stress 0.177416
## ... Procrustes: rmse 0.001394726 max resid 0.03334204
## Run 498 stress 0.1776576
## ... Procrustes: rmse 0.002721976 max resid 0.04809881
## Run 499 stress 0.1780637
## Run 500 stress 0.1780339
## Run 501 stress 0.1801157
## Run 502 stress 0.1780711
## Run 503 stress 0.1782811
## Run 504 stress 0.1784319
## Run 505 stress 0.1778694
## ... Procrustes: rmse 0.003494776 max resid 0.04883086
## Run 506 stress 0.1781149
## Run 507 stress 0.1782857
## Run 508 stress 0.1780105
## Run 509 stress 0.1784781
## Run 510 stress 0.1774253
## ... Procrustes: rmse 0.001961433 max resid 0.04802876
## Run 511 stress 0.1780116
## Run 512 stress 0.1775577
## ... Procrustes: rmse 0.002527085 max resid 0.05552912
## Run 513 stress 0.17744
## ... Procrustes: rmse 0.003394542 max resid 0.06849695
## Run 514 stress 0.179441
## Run 515 stress 0.1846036
## Run 516 stress 0.1778328
## ... Procrustes: rmse 0.004841648 max resid 0.09193745
## Run 517 stress 0.1785876
## Run 518 stress 0.1776837
## ... Procrustes: rmse 0.003394212 max resid 0.05567924
## Run 519 stress 0.1780553
## Run 520 stress 0.1781954
## Run 521 stress 0.1778907
## ... Procrustes: rmse 0.003347422 max resid 0.06094146
## Run 522 stress 0.1779159
## Run 523 stress 0.1780089
## Run 524 stress 0.1777838
## ... Procrustes: rmse 0.004328924 max resid 0.09148067
## Run 525 stress 0.1781193
## Run 526 stress 0.1783959
## Run 527 stress 0.1853264
## Run 528 stress 0.1778778
## ... Procrustes: rmse 0.003210746 max resid 0.06072642
## Run 529 stress 0.1775597
## ... Procrustes: rmse 0.002768285 max resid 0.05552782
## Run 530 stress 0.1780208
## Run 531 stress 0.1834085
## Run 532 stress 0.1836491
## Run 533 stress 0.1785632
## Run 534 stress 0.1781594
## Run 535 stress 0.1780607
## Run 536 stress 0.1774352
## ... Procrustes: rmse 0.002701482 max resid 0.06807014
## Run 537 stress 0.1777169
## ... Procrustes: rmse 0.004036411 max resid 0.09188084
## Run 538 stress 0.1783778
## Run 539 stress 0.1777472
## ... Procrustes: rmse 0.004126224 max resid 0.05552435
## Run 540 stress 0.1780673
## Run 541 stress 0.1778467
## ... Procrustes: rmse 0.00407051 max resid 0.09029964
## Run 542 stress 0.1777365
## ... Procrustes: rmse 0.004200583 max resid 0.09062605
## Run 543 stress 0.1779558
## Run 544 stress 0.1775604
## ... Procrustes: rmse 0.0021874 max resid 0.05543686
## Run 545 stress 0.1784593
## Run 546 stress 0.1788613
## Run 547 stress 0.1781871
## Run 548 stress 0.1775668
## ... Procrustes: rmse 0.002676124 max resid 0.05565022
## Run 549 stress 0.1779129
## ... Procrustes: rmse 0.003759624 max resid 0.06748669
## Run 550 stress 0.1785634
## Run 551 stress 0.1775574
## ... Procrustes: rmse 0.002579593 max resid 0.05554672
## Run 552 stress 0.1778842
## ... Procrustes: rmse 0.00280287 max resid 0.06083177
## Run 553 stress 0.1784105
## Run 554 stress 0.1778349
## ... Procrustes: rmse 0.004719888 max resid 0.0680714
## Run 555 stress 0.1781432
## Run 556 stress 0.1783364
## Run 557 stress 0.1780231
## Run 558 stress 0.1842986
## Run 559 stress 0.1781545
## Run 560 stress 0.1778936
## ... Procrustes: rmse 0.003992288 max resid 0.08954685
## Run 561 stress 0.1776055
## ... Procrustes: rmse 0.003757768 max resid 0.06730644
## Run 562 stress 0.1776336
## ... Procrustes: rmse 0.003800441 max resid 0.06859831
## Run 563 stress 0.1803568
## Run 564 stress 0.1782824
## Run 565 stress 0.1790443
## Run 566 stress 0.1784576
## Run 567 stress 0.1782256
## Run 568 stress 0.1779315
## Run 569 stress 0.1783002
## Run 570 stress 0.1847469
## Run 571 stress 0.1783999
## Run 572 stress 0.1775767
## ... Procrustes: rmse 0.002893037 max resid 0.05530496
## Run 573 stress 0.1781932
## Run 574 stress 0.1776486
## ... Procrustes: rmse 0.004048372 max resid 0.06895944
## Run 575 stress 0.1781685
## Run 576 stress 0.1779423
## Run 577 stress 0.1777989
## ... Procrustes: rmse 0.002959184 max resid 0.05619753
## Run 578 stress 0.1784295
## Run 579 stress 0.1780679
## Run 580 stress 0.1785393
## Run 581 stress 0.1774338
## ... Procrustes: rmse 0.002219565 max resid 0.04587605
## Run 582 stress 0.1782662
## Run 583 stress 0.1781619
## Run 584 stress 0.1774156
## ... Procrustes: rmse 0.001646877 max resid 0.03318895
## Run 585 stress 0.1774984
## ... Procrustes: rmse 0.003713014 max resid 0.06864332
## Run 586 stress 0.1776057
## ... Procrustes: rmse 0.003951453 max resid 0.06768039
## Run 587 stress 0.1785065
## Run 588 stress 0.1782642
## Run 589 stress 0.177637
## ... Procrustes: rmse 0.003337114 max resid 0.05568245
## Run 590 stress 0.1786869
## Run 591 stress 0.1778828
## ... Procrustes: rmse 0.004536248 max resid 0.06898516
## Run 592 stress 0.1776678
## ... Procrustes: rmse 0.003890249 max resid 0.06875146
## Run 593 stress 0.1786463
## Run 594 stress 0.1787425
## Run 595 stress 0.1780064
## Run 596 stress 0.1781563
## Run 597 stress 0.1776504
## ... Procrustes: rmse 0.002075973 max resid 0.04616142
## Run 598 stress 0.1777225
## ... Procrustes: rmse 0.004502796 max resid 0.06891501
## Run 599 stress 0.1777584
## ... Procrustes: rmse 0.004814307 max resid 0.09174764
## Run 600 stress 0.1778969
## ... Procrustes: rmse 0.004083762 max resid 0.06821547
## Run 601 stress 0.1778303
## ... Procrustes: rmse 0.004840649 max resid 0.0896787
## Run 602 stress 0.1778762
## ... Procrustes: rmse 0.003178795 max resid 0.06070006
## Run 603 stress 0.1788108
## Run 604 stress 0.1784395
## Run 605 stress 0.1783699
## Run 606 stress 0.1782776
## Run 607 stress 0.1786747
## Run 608 stress 0.1774276
## ... Procrustes: rmse 0.001936277 max resid 0.04809901
## Run 609 stress 0.1780704
## Run 610 stress 0.1786777
## Run 611 stress 0.1781872
## Run 612 stress 0.1777508
## ... Procrustes: rmse 0.004519395 max resid 0.0900355
## Run 613 stress 0.1774274
## ... Procrustes: rmse 0.001980451 max resid 0.04832022
## Run 614 stress 0.1777095
## ... Procrustes: rmse 0.003927239 max resid 0.0909832
## Run 615 stress 0.1777821
## ... Procrustes: rmse 0.004086101 max resid 0.09013569
## Run 616 stress 0.1779509
## Run 617 stress 0.1783463
## Run 618 stress 0.1783724
## Run 619 stress 0.1821289
## Run 620 stress 0.1781852
## Run 621 stress 0.1782656
## Run 622 stress 0.1792295
## Run 623 stress 0.1779862
## Run 624 stress 0.1781629
## Run 625 stress 0.1779717
## Run 626 stress 0.1832798
## Run 627 stress 0.1777398
## ... Procrustes: rmse 0.004710765 max resid 0.08636559
## Run 628 stress 0.177974
## Run 629 stress 0.178333
## Run 630 stress 0.1786586
## Run 631 stress 0.1779424
## Run 632 stress 0.1781727
## Run 633 stress 0.1774336
## ... Procrustes: rmse 0.002731946 max resid 0.06815579
## Run 634 stress 0.1792466
## Run 635 stress 0.1783372
## Run 636 stress 0.1780012
## Run 637 stress 0.1780348
## Run 638 stress 0.1779719
## Run 639 stress 0.1782869
## Run 640 stress 0.1784866
## Run 641 stress 0.17833
## Run 642 stress 0.178006
## Run 643 stress 0.1782195
## Run 644 stress 0.1794773
## Run 645 stress 0.17798
## Run 646 stress 0.1784071
## Run 647 stress 0.1778025
## ... Procrustes: rmse 0.003656818 max resid 0.06861268
## Run 648 stress 0.1791976
## Run 649 stress 0.1788675
## Run 650 stress 0.1785444
## Run 651 stress 0.1779663
## Run 652 stress 0.177835
## ... Procrustes: rmse 0.002929232 max resid 0.05669957
## Run 653 stress 0.1790469
## Run 654 stress 0.1787268
## Run 655 stress 0.1782342
## Run 656 stress 0.1850389
## Run 657 stress 0.1838549
## Run 658 stress 0.1796082
## Run 659 stress 0.1782143
## Run 660 stress 0.1780416
## Run 661 stress 0.1774157
## ... Procrustes: rmse 0.001416552 max resid 0.03248838
## Run 662 stress 0.178056
## Run 663 stress 0.1781368
## Run 664 stress 0.1779726
## Run 665 stress 0.1779071
## ... Procrustes: rmse 0.004193271 max resid 0.06779173
## Run 666 stress 0.1783915
## Run 667 stress 0.1774405
## ... Procrustes: rmse 0.003295205 max resid 0.06829124
## Run 668 stress 0.1783319
## Run 669 stress 0.1780297
## Run 670 stress 0.1787187
## Run 671 stress 0.1782942
## Run 672 stress 0.1780348
## Run 673 stress 0.1779311
## Run 674 stress 0.1778625
## ... Procrustes: rmse 0.004495841 max resid 0.0894893
## Run 675 stress 0.1774557
## ... Procrustes: rmse 0.003472369 max resid 0.06826293
## Run 676 stress 0.1778838
## ... Procrustes: rmse 0.004413189 max resid 0.06872585
## Run 677 stress 0.1781666
## Run 678 stress 0.1776314
## ... Procrustes: rmse 0.004074883 max resid 0.06719819
## Run 679 stress 0.1782726
## Run 680 stress 0.1780292
## Run 681 stress 0.1774474
## ... Procrustes: rmse 0.003055974 max resid 0.06778122
## Run 682 stress 0.1780774
## Run 683 stress 0.1774388
## ... Procrustes: rmse 0.001932139 max resid 0.04765429
## Run 684 stress 0.1781235
## Run 685 stress 0.1775016
## ... Procrustes: rmse 0.002179999 max resid 0.03567669
## Run 686 stress 0.1783594
## Run 687 stress 0.1782501
## Run 688 stress 0.1795764
## Run 689 stress 0.1780483
## Run 690 stress 0.178061
## Run 691 stress 0.1801184
## Run 692 stress 0.1776575
## ... Procrustes: rmse 0.002537222 max resid 0.04572514
## Run 693 stress 0.1795844
## Run 694 stress 0.1782758
## Run 695 stress 0.1779979
## Run 696 stress 0.1787616
## Run 697 stress 0.1775795
## ... Procrustes: rmse 0.003054286 max resid 0.05534603
## Run 698 stress 0.1782055
## Run 699 stress 0.1779628
## Run 700 stress 0.1783335
## Run 701 stress 0.1788936
## Run 702 stress 0.1779378
## Run 703 stress 0.1779714
## Run 704 stress 0.1778686
## ... Procrustes: rmse 0.002382468 max resid 0.06028701
## Run 705 stress 0.1783212
## Run 706 stress 0.178365
## Run 707 stress 0.1784547
## Run 708 stress 0.1777017
## ... Procrustes: rmse 0.003852875 max resid 0.05544873
## Run 709 stress 0.1779996
## Run 710 stress 0.177856
## ... Procrustes: rmse 0.004014056 max resid 0.0686567
## Run 711 stress 0.1795079
## Run 712 stress 0.178204
## Run 713 stress 0.1782112
## Run 714 stress 0.1787307
## Run 715 stress 0.1781106
## Run 716 stress 0.1782829
## Run 717 stress 0.1781663
## Run 718 stress 0.1782431
## Run 719 stress 0.1784432
## Run 720 stress 0.1783531
## Run 721 stress 0.1790782
## Run 722 stress 0.1780046
## Run 723 stress 0.1777383
## ... Procrustes: rmse 0.004705096 max resid 0.08735041
## Run 724 stress 0.1779654
## Run 725 stress 0.1784175
## Run 726 stress 0.1781411
## Run 727 stress 0.1778147
## ... Procrustes: rmse 0.003186519 max resid 0.05636683
## Run 728 stress 0.1776042
## ... Procrustes: rmse 0.003931106 max resid 0.06770664
## Run 729 stress 0.1785373
## Run 730 stress 0.1782838
## Run 731 stress 0.1779193
## Run 732 stress 0.1784005
## Run 733 stress 0.1779873
## Run 734 stress 0.1784939
## Run 735 stress 0.1782922
## Run 736 stress 0.1781383
## Run 737 stress 0.1779047
## ... Procrustes: rmse 0.004791254 max resid 0.06938596
## Run 738 stress 0.1786606
## Run 739 stress 0.1780269
## Run 740 stress 0.1777943
## ... Procrustes: rmse 0.00443056 max resid 0.06930537
## Run 741 stress 0.1778865
## ... Procrustes: rmse 0.003375055 max resid 0.04961808
## Run 742 stress 0.1785981
## Run 743 stress 0.1791062
## Run 744 stress 0.1776861
## ... Procrustes: rmse 0.003988322 max resid 0.06875822
## Run 745 stress 0.178571
## Run 746 stress 0.1840914
## Run 747 stress 0.1780671
## Run 748 stress 0.1780551
## Run 749 stress 0.1808754
## Run 750 stress 0.1830386
## Run 751 stress 0.1782095
## Run 752 stress 0.1776058
## ... Procrustes: rmse 0.003915556 max resid 0.0676448
## Run 753 stress 0.1779216
## Run 754 stress 0.1780735
## Run 755 stress 0.1778547
## ... Procrustes: rmse 0.003295145 max resid 0.05558898
## Run 756 stress 0.1784352
## Run 757 stress 0.1774934
## ... Procrustes: rmse 0.003266585 max resid 0.06827032
## Run 758 stress 0.1779717
## Run 759 stress 0.1775608
## ... Procrustes: rmse 0.002221883 max resid 0.05542316
## Run 760 stress 0.177938
## Run 761 stress 0.1785127
## Run 762 stress 0.1782136
## Run 763 stress 0.1778602
## ... Procrustes: rmse 0.003353873 max resid 0.05683174
## Run 764 stress 0.1776089
## ... Procrustes: rmse 0.002420601 max resid 0.04823628
## Run 765 stress 0.1781498
## Run 766 stress 0.1789868
## Run 767 stress 0.1778145
## ... Procrustes: rmse 0.003865261 max resid 0.06838026
## Run 768 stress 0.1799941
## Run 769 stress 0.177943
## Run 770 stress 0.1784645
## Run 771 stress 0.1792511
## Run 772 stress 0.1777535
## ... Procrustes: rmse 0.004599872 max resid 0.08917557
## Run 773 stress 0.1779781
## Run 774 stress 0.1779611
## Run 775 stress 0.178292
## Run 776 stress 0.1781133
## Run 777 stress 0.1776054
## ... Procrustes: rmse 0.003716908 max resid 0.0670931
## Run 778 stress 0.1784789
## Run 779 stress 0.1777624
## ... Procrustes: rmse 0.004890134 max resid 0.08996975
## Run 780 stress 0.1781186
## Run 781 stress 0.178353
## Run 782 stress 0.1778677
## ... Procrustes: rmse 0.005027039 max resid 0.0925226
## Run 783 stress 0.1780809
## Run 784 stress 0.1778967
## ... Procrustes: rmse 0.004159541 max resid 0.06840989
## Run 785 stress 0.1779847
## Run 786 stress 0.1778847
## ... Procrustes: rmse 0.003317148 max resid 0.06084889
## Run 787 stress 0.1784183
## Run 788 stress 0.17823
## Run 789 stress 0.1782843
## Run 790 stress 0.1782948
## Run 791 stress 0.1784138
## Run 792 stress 0.1781473
## Run 793 stress 0.1781581
## Run 794 stress 0.1777783
## ... Procrustes: rmse 0.003929035 max resid 0.09024975
## Run 795 stress 0.1786613
## Run 796 stress 0.1777334
## ... Procrustes: rmse 0.004244739 max resid 0.08619678
## Run 797 stress 0.1779981
## Run 798 stress 0.1782563
## Run 799 stress 0.178902
## Run 800 stress 0.1774131
## ... New best solution
## ... Procrustes: rmse 0.000303372 max resid 0.007033784
## ... Similar to previous best
## *** Solution reached##
## Call:
## metaMDS(comm = NoncoastalFive[, 6:107], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NoncoastalFive[, 6:107]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1774131
## Stress type 1, weak ties
## Two convergent solutions found after 800 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NoncoastalFive[, 6:107]'
Plot with Stations: Non-Coastal
Season: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Outside Sample Window Spring
## delta 0.626 0.5343 0.619
## n 346 8 338
##
## Chance corrected within-group agreement A: 0.04984
## Based on observed delta 0.6215 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Ecoregion: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Northern Piedmont Piedmont
## delta 0.5948 0.6046 0.641 0.6106
## n 154 40 101 138
## Ridge and Valley
## delta 0.6556
## n 259
##
## Chance corrected within-group agreement A: 0.03989
## Based on observed delta 0.628 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Basin: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Middle James-Upper New Potomac-Lower
## delta 0.5234 0.533 0.6097 0.651 0.6508 0.6374
## n 12 4 61 120 78 25
## Potomac-Shenandoah Rappahannock Roanoke Tennessee-Big Sandy
## delta 0.6561 0.6355 0.6096 0.6011
## n 42 122 87 16
## Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.626 0.626 0.5727 0.5898
## n 50 53 4 18
##
## Chance corrected within-group agreement A: 0.03776
## Based on observed delta 0.6294 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Admin Region: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO VRO
## delta 0.6415 0.651 0.5798 0.633 0.6428
## n 250 158 18 156 110
##
## Chance corrected within-group agreement A: 0.02106
## Based on observed delta 0.6403 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999##Bioregion: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$Bioregion, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Mountain Piedmont
## delta 0.6469 0.6336
## n 453 239
##
## Chance corrected within-group agreement A: 0.01805
## Based on observed delta 0.6423 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
Sample Method: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.5603 0.6532
## n 9 683
##
## Chance corrected within-group agreement A: 0.003217
## Based on observed delta 0.652 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Stream Order: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5
## delta 0.6262 0.6549 0.6195 0.5738 0.5392
## n 244 205 137 79 27
##
## Chance corrected within-group agreement A: 0.04604
## Based on observed delta 0.624 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Water Quality Standard Class: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:107], grouping = samplescoresenv_noncoast$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI
## delta 0.6371 0.6442 0.6313 0.6033
## n 211 185 87 209
##
## Chance corrected within-group agreement A: 0.03981
## Based on observed delta 0.6281 and expected delta 0.6541
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Natural Trout Water WQS: Non-Coastal
